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author_block one-internal-gutter"><div class="uncol style-light" ><div class="uncoltable"><div class="uncell no-block-padding" ><div class="uncont"><div class="uncode-info-box top-avatar" ><span class="author-wrap"><a href="https://blog.mdpi.com/author/mdpimag/"><span class="uncode-ib-avatar uncode-ib-avatar-size-xl"><img alt='MDPI Magazine' src='https://mdpiblog.wordpress.sciforum.net/wp-content/uploads/sites/4/2021/10/defaultavatar.png' srcset='https://mdpiblog.wordpress.sciforum.net/wp-content/uploads/sites/4/2021/10/defaultavatar.png 2x' class='avatar avatar-80 photo avatar-default' height='80' width='80' loading='lazy' decoding='async'/></span></a><span class="author-info"> <a href="https://blog.mdpi.com/author/mdpimag/">MDPI Magazine</a></span></span><span class="uncode-ib-separator"></span><span class="date-info">13 June 2014</span><span class="uncode-ib-separator"></span><span class="category-info"> <a href="https://blog.mdpi.com/category/open-science/" title="View all posts in Open Science" class="">Open Science</a></span></div></div></div></div></div></div><div class="wpb_column pos-top pos-center align_left column_parent col-lg-8 single-internal-gutter"><div class="uncol style-light" ><div class="uncoltable"><div class="uncell no-block-padding" ><div class="uncont"><div class="uncode-single-media post_heading_image text-left"><div class="single-wrapper" style="max-width: 100%;"><div class="tmb tmb-light tmb-media-first tmb-media-last tmb-content-overlay tmb-no-bg"> <div class="t-inside"><div class="t-entry-visual"><div class="t-entry-visual-tc"><div class="uncode-single-media-wrapper"> <img decoding="async" class="adaptive-async wp-image-11428" src="https://mdpiblog.wordpress.sciforum.net/wp-content/uploads/sites/4/2014/06/In-Silico-Docking-of-Bolinaquinone-at-Clathrin-Terminal-Domain-scaled-uai-258x135.jpg" width="258" height="135" alt="Banner for bolinaquinone article." data-uniqueid="11428-797002" data-guid="https://mdpiblog.wordpress.sciforum.net/wp-content/uploads/sites/4/2014/06/In-Silico-Docking-of-Bolinaquinone-at-Clathrin-Terminal-Domain-scaled.jpg" data-path="2014/06/In-Silico-Docking-of-Bolinaquinone-at-Clathrin-Terminal-Domain-scaled.jpg" data-width="2560" data-height="1336" data-singlew="8" data-singleh="" data-crop="" data-fixed=""></div> </div> </div></div> </div></div></div><div class="vc_custom_heading_wrap "><div class="heading-text el-text" ><h2 class="h2" ><span>In Silico Docking of Bolinaquinone at Clathrin Terminal Domain</span></h2></div><div class="clear"></div></div><div class="uncode_text_column" ><p><em>Guest Commentary by Derek McPhee</em></p> <p>Endocytosis is a fundamental process that delivers macromolecules located outside the cell or on the cell membrane to the cytoplasm. It is a necessary process for nutrients to reach the cell, and for regulation of numerous transmembrane receptors. Of the various ways that cargo can access the cytoplasm, so called clathrin-dependent endocytosis is one of the most studied. This mechanism is generally well understood. Membrane fragments, along with their contents, enter the cell as vesicles coated with clathrin species. This activity is key to the survival and normal functioning of eukaryotic cells. It also has also been associated with a variety of pathological states. These include the access of pathogens like virus and bacteria to the cell interior, a number of cancers and other conditions.</p> <p><img fetchpriority="high" decoding="async" class="alignnone size-medium wp-image-1815" src="https://mdpimag.files.wordpress.com/2014/06/molecules-19-06609-ag.gif?w=300" alt="molecules-19-06609-ag" width="300" height="239" /></p> <h2>Bolinaquinone</h2> <p>Bolinaquinone, is a cytotoxic marine sesquiterpene hydroquinone first isolated by de Guzman <em>et al</em>. in 1998 from a Phillipine <em>Dysidea </em>sponge, and later shown to be a clathrin inhibitor. Its relatively simple structure makes it an attractive target for systematic structural modification to enhance or change its biological activity, but details of its interaction with clathrin were lacking.</p> <p>To fill this gap in our knowledge, we now have the Abdel-Hamid and McCluskey <a href="https://www.mdpi.com/journal/molecules"><em>Molecules</em></a> paper, “<a href="https://www.mdpi.com/1420-3049/19/5/6609"><em>In Silico </em>Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site</a>”.</p> <h3>Docking of bolinaquinone</h3> <p>Building upon their earlier experience studying the binding site and mode of action of other small molecule inhibitors of clathrin, the authors systematically examined the docking of bolinaquinone in the clathrin terminal domain. This approach revealed that bolinaquinone appears to occupy a binding pocket distinct from that occupied by previously identified inhibitors. Exhaustive flexible docking studies and examination of the stability of docked poses and interaction energies allowed the authors to identify up to five binding sites, and propose the most likely one, thus demonstrating the flexibility and power of this virtual screening approach. The identification of the key functional group interactions should provide a most valuable guide for synthetic chemists aiming to design simplified bolinaquinone analogs to either confirm the putative binding site or as novel therapeutic agents in any of the pathologies where clathrin is known to play a key role.</p> <h2>References</h2> <div class="reference"> <ul> <li>de Guzman, F.S.; Copp, B.R.; Mayne, C.L.; Concepcion, G.P.; Mangalindan, G.C.; Barrows, L.R.; Ireland, C.M. <a href="https://pubs.acs.org/doi/abs/10.1021/jo981037t?journalCode=joceah">Bolinaquinone: A novel cytotoxic sesquiterpene hydroxyquinone from a Philippine Dysidea sponge</a>. <em>J. Org. Chem</em>. <strong>1998</strong>, 63, 8042–8044.</li> <li>Abdel-Hamid, M.K.; McCluskey, A. <a href="https://www.mdpi.com/1420-3049/19/5/6609"><i>In Silico</i> Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site</a>. <em>Molecules</em> <b>2014</b>, <em>19</em>, 6609-6622.</li> </ul> </div> <div class="bio"><em><img decoding="async" class="wp-image-1833 size-thumbnail aligncenter" src="https://mdpimag.files.wordpress.com/2014/06/me-kyoto-small1.jpg?w=122" alt="Derek McPhee" width="122" height="150" /></em></div> <div class="bio">Derek McPhee is the Editor-in-Chief of the journal<em> <a href="https://www.mdpi.com/journal/molecules">Molecules</a></em>. He has a Lic.C. degree in Applied Chemistry from the Universidad de Málaga (Spain) and also his Ph.D. in Organic Chemistry from the University of Calgary (Canada), and is currently the Senior Director of Technology Strategy at Amyris Inc., a biotechnology company focused on the production of renewable alternatives to petroleum-based fuels and specialty chemicals.</div> </div></div></div></div></div></div><div class="wpb_column pos-top pos-center align_left column_parent col-lg-2 no-internal-gutter"><div class="uncol style-light" ><div class="uncoltable"><div class="uncell no-block-padding" ><div class="uncont"> <div class="wpb_raw_code wpb_content_element wpb_raw_html share_sidebar" > <div class="wpb_wrapper"> <div class="wpulike wpulike-default " ><div class="wp_ulike_general_class wp_ulike_is_not_liked"><button type="button" aria-label="Like Button" data-ulike-id="1813" data-ulike-nonce="ec776b8ea1" data-ulike-type="post" data-ulike-template="wpulike-default" 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